adding-linkouts.RmdThis vignette demonstrates how to add linkouts to a NG-CHM. Linkouts allow for a deeper exploration of the NG-CHM data, for example by providing direct links to NCBI Databases, GeneCards, etc.
The needed packages are loaded and a basic NG-CHM is constructed from the sample data.
library(NGCHMDemoData)
library(NGCHM)
hm <- chmNew('tcga-brca', TCGA.BRCA.ExpressionData)To add linkouts, the axis type is specified with
chmAddAxisType(). For the demo data in this example, row
labels correspond to genes, and are specified as HUGO gene symbols:
hm <- chmAddAxisType(hm, 'row', 'bio.gene.hugo')The column labels in the demo data are full 28-character TCGA aliquot barcodes:
hm <- chmAddAxisType(hm, 'column', 'bio.tcga.barcode.sample.vial.portion.analyte.aliquot')In the above example, the axis type was ‘bio.gene.hugo’. The available axis types are: